The open source Linux graphics drivers support the new graphics chip generation already - this is a novelty, because in the recent past it took at least months, to the open source drivers are unable to attract new GPUs. Rosy the situation is not yet, because the appropriate drivers stuck so far only in pre-release versions of the Linux kernel 4.7, 12.0 and Mesa LLVM 3.8.1 / 3.9. However, these versions should appear in the next few weeks, so Ubuntu 10.16 should and other distributions appearing in autumn supported the new graphics cards from home. Until then, there are also still eliminate some detail problems, because the brief test with development versions of the Linux kernel and the image of Mesa Radeon RX 480 flickered now and then; AMD's open-source developers are discussing but just a few corrections that eliminate this problem if possible.

If it's really too much trouble, we might indeed better opt for a soldered in GPU. Then of course, we'll have to decide on a GPU. I don't think we'd have the resources to offer multiple configurations.

How about making a mainboard with a MXM slot and a default MXM card?

You can also test other MXM cards available to verify that the slot works as intended.

Then you get working device with a card of your choice and people are free to swap in a different card.

Or you can start shipping a different model with a different card later.